We have an existing flock of 26 hens (9 bantams, barred rocks, golden comets, partridge rocks) and one barred rock rooster. The rooster is a year and a half old. We had a second rooster that we got at the same time as our BR (we got them as day old chicks) but he died in May.

We wanted to add to our flock and made arrangements to get 20 6 month old hens - 5 Easter Eggers and 5 Black Australorps. We picked them up today. When we got them home and out of the crates, we discovered that one of the Black Australorps was really a rooster.

We had not planned on a second rooster but we got one. The new chickens are in quarantine in our hoophouse. After quarantine, what is the best way to introduce the new rooster to the old one? We've introduced new hens before and have no problem with it. We've also had meat birds free range with our layers and rooster and there was never a problem there. Should we be concerned that this will be a different experience?

Also, how long should we quarantine? We didn't quarantine our bantams when we got them but realize that we should have just to be safe. My husband was thinking a week - I wasn't sure if that was long enough...

Well, I just let mine out and watch them. Sometimes they fight, sometimes they don't. I'd say put the new rooster in a carrier and make sure the old rooster can see him - once they stop fighting (given they do) let the new one out.
Always supervise. Fighting can be very dangerous for big birds like yours ^^

For a true medical quarantine, it's something like 30 days at 30 feet away minimum.
Tend new birds last and keep separate shoes for new and old birds so you don't cross contaminate the areas.

After 30 days or however long you choose, it's nice if you can keep them physically separate but within sight of one another for another week or so...then let them out free range and watch closely as there will be some fighting to establish pecking order.

Do some searching and reading to get other ideas on how to handle the situation, there are lots of different techniques for different situations.

Best way I've found to search for a specific topic is use the advanced search function.

If I read the OP correctly......she now has 46 hens and 2 roosters or maybe it should 36 hens and 2 roosters.

Either way, that's a lot of hens for one boy......so if they can coexist, why not?

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I just don't see the point in keeping a bird you didn't want in the first place. And yes, it's a lot of hens, but in my opinion why go through the bother? The roosters are still going to clash to some degree. I just think folks get in the mindset of "I have to keep this bird even though I didn't want a male and just got screwed" way too often.